TECH_DEBT: Clinical Reasoning and HAPI Dependency Update

Java/measureeval/pom.xml

@@ -95,22 +95,14 @@
             <scope>runtime</scope>
         </dependency>
 
-        <dependency>
-            <groupId>info.cqframework</groupId>
-            <artifactId>engine</artifactId>
-            <version>3.15.0</version>
-        </dependency>
-
         <dependency>
             <groupId>org.opencds.cqf.fhir</groupId>
-            <artifactId>cqf-fhir-cr</artifactId>
+            <artifactId>cqf-fhir-cql</artifactId>
         </dependency>
 
-
         <dependency>
             <groupId>org.opencds.cqf.fhir</groupId>
-            <artifactId>cqf-fhir-jackson</artifactId>
-            <type>pom</type>
+            <artifactId>cqf-fhir-cr</artifactId>
         </dependency>
 
         <!-- for logback to use conditional expressions -->

Java/measureeval/src/main/java/com/lantanagroup/link/measureeval/services/MeasureEvaluator.java

@@ -4,17 +4,19 @@
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
 import com.lantanagroup.link.measureeval.repositories.LinkInMemoryFhirRepository;
+import com.lantanagroup.link.measureeval.utils.DateUtils;
 import com.lantanagroup.link.measureeval.utils.ParametersUtils;
 import com.lantanagroup.link.measureeval.utils.StreamUtils;
 import lombok.Getter;
 import org.cqframework.cql.cql2elm.LibraryBuilder;
 import org.hl7.fhir.r4.model.*;
-import org.opencds.cqf.fhir.api.Repository;
 import org.opencds.cqf.fhir.cql.EvaluationSettings;
 import org.opencds.cqf.fhir.cql.engine.retrieve.RetrieveSettings;
 import org.opencds.cqf.fhir.cql.engine.terminology.TerminologySettings;
 import org.opencds.cqf.fhir.cr.measure.MeasureEvaluationOptions;
+import org.opencds.cqf.fhir.cr.measure.common.MeasurePeriodValidator;
 import org.opencds.cqf.fhir.cr.measure.r4.R4MeasureService;
+import org.opencds.cqf.fhir.cr.measure.r4.utils.R4MeasureServiceUtils;
 import org.opencds.cqf.fhir.utility.monad.Eithers;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -106,12 +108,13 @@ private MeasureReport doEvaluate(
             DateTimeType periodEnd,
             StringType subject,
             Bundle additionalData) {
-        Repository repository = new LinkInMemoryFhirRepository(fhirContext, bundle);
-        R4MeasureService measureService = new R4MeasureService(repository, options);
+        var repository = new LinkInMemoryFhirRepository(fhirContext, bundle);
+        R4MeasureService measureService = new R4MeasureService(repository, options, new MeasurePeriodValidator());
+
         return measureService.evaluate(
                 Eithers.forRight3(measure),
-                periodStart == null ? null : periodStart.asStringValue(),
-                periodEnd == null ? null : periodEnd.asStringValue(),
+                periodStart == null ? null : DateUtils.getZonedDateTime(periodStart),
+                periodEnd == null ? null : DateUtils.getZonedDateTime(periodEnd),
                 null,
                 subject.asStringValue(),
                 null,

Java/measureeval/src/main/java/com/lantanagroup/link/measureeval/utils/DateUtils.java

@@ -0,0 +1,22 @@
+package com.lantanagroup.link.measureeval.utils;
+
+import org.hl7.fhir.r4.model.DateTimeType;
+
+import java.time.Instant;
+import java.time.ZoneId;
+import java.time.ZonedDateTime;
+
+public class DateUtils {
+
+    public static ZonedDateTime getZonedDateTime(DateTimeType dateTime) {
+        if (dateTime == null) {
+            return null;
+        }
+        var zoneId = dateTime.getTimeZone() == null ? ZoneId.systemDefault() : dateTime.getTimeZone().toZoneId();
+        return getZonedDateTime(dateTime.getValue().toInstant(), zoneId);
+    }
+
+    public static ZonedDateTime getZonedDateTime(Instant instant, ZoneId zoneId) {
+        return ZonedDateTime.ofInstant(instant, zoneId);
+    }
+}

Java/measureeval/src/test/java/com/lantanagroup/link/measureeval/services/CqlLibraries.java

@@ -128,66 +128,25 @@ define function ConditionResource(condition Condition):
               false""";
 
     public static final String SIMPLE_PROPORTION_ALL_FALSE = """
-            library ProportionLibraryFalse version '1.0.0'
-                            
+            library ProportionLibraryAllFalse version '1.0.0'
+
             using FHIR version '4.0.1'
-                            
+
             context Patient
 
             define "Initial Population":
               false
-              
+
             define "Numerator":
               false
-              
+
             define "Numerator Exclusion":
               false
-                            
+
             define "Denominator":
               false
-              
+
             define "Denominator Exclusion":
               false""";
 
-    public static final String SIMPLE_RATIO = """
-            library RatioLibrary version '1.0.0'
-
-            using FHIR version '4.0.1'
-
-            context Patient
-
-            define "Initial Population":
-              ["Encounter"]
-
-            define "Numerator":
-              "Initial Population"
-
-            define "Denominator":
-              "Initial Population"
-
-            define function "Denominator Observation"(Encounter "Encounter"):
-              24
-
-            define function "Numerator Observation"(Encounter "Encounter"):
-              1""";
-
-    public static final String SIMPLE_CONTINUOUS_VARIABLE = """
-            library ContinuousVariableLibrary version '1.0.0'
-
-            using FHIR version '4.0.1'
-
-            context Patient
-
-            define "Initial Population":
-              ["Encounter"]
-
-            define "Measure Population":
-              "Initial Population"
-
-            define "Measure Population Exclusion":
-              false
-
-            define function "Measure Observation"(Encounter "Encounter"):
-              24""";
-
 }

Java/measureeval/src/test/java/com/lantanagroup/link/measureeval/services/KnowledgeArtifactBuilder.java

@@ -237,7 +237,9 @@ static class CohortMeasureWithValueSetTrue {
          * @return A {@link Measure} resource with the cohort scoring type and an initial population definition.
          */
         public static Measure measure() {
-            return MeasureBuilder.build(MEASURE_ID, MEASURE_URL, LIBRARY_URL, "cohort", MeasurePopulationGroup.initialPopulation());
+            var measure = MeasureBuilder.build(MEASURE_ID, MEASURE_URL, LIBRARY_URL, "cohort", MeasurePopulationGroup.initialPopulation());
+            measure.addExtension("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-populationBasis", new CodeType("Encounter"));
+            return measure;
         }
 
         /**
@@ -418,90 +420,6 @@ public static Bundle bundle() {
         }
     }
 
-    /**
-     * Nested utility class for building resources for a "Simple Ratio Measure" scenario.
-     * This class creates a {@link Measure}, {@link Library}, and {@link Bundle} to represent a ratio measure
-     * with an initial population, numerator, and denominator, including exclusions.
-     */
-    static class SimpleRatioMeasure {
-        private static final String MEASURE_ID = "RatioMeasure";
-        private static final String LIBRARY_ID = "RatioLibrary";
-        private static final String MEASURE_URL = BASE_MEASURE_URL + MEASURE_ID;
-        private static final String LIBRARY_URL = BASE_LIBRARY_URL + LIBRARY_ID;
-
-        /**
-         * Builds the {@link Measure} resource for the "Simple Ratio Measure" scenario.
-         * The measure is configured with the ratio scoring type, an initial population, numerator, and denominator,
-         * including numerator and denominator exclusions.
-         *
-         * @return A {@link Measure} resource with the ratio scoring type and specified population groups.
-         */
-        public static Measure measure() {
-            return MeasureBuilder.build(MEASURE_ID, MEASURE_URL, LIBRARY_URL, "ratio", MeasurePopulationGroup.initialPopulation(), MeasurePopulationGroup.numerator(), MeasurePopulationGroup.numeratorExclusion(), MeasurePopulationGroup.denominator(), MeasurePopulationGroup.denominatorExclusion());
-        }
-
-        /**
-         * Builds the {@link Library} resource for the "Simple Ratio Measure" scenario.
-         * The library contains CQL logic for evaluating the measure.
-         *
-         * @return A {@link Library} resource containing CQL logic for the ratio measure.
-         */
-        public static Library library() {
-            return LibraryBuilder.build(LIBRARY_ID, "1.0.0", LIBRARY_ID, LIBRARY_URL, CqlLibraries.SIMPLE_RATIO);
-        }
-
-        /**
-         * Builds a {@link Bundle} resource containing the {@link Measure} and {@link Library} for the "Simple Ratio Measure" scenario.
-         *
-         * @return A {@link Bundle} resource containing the measure and library.
-         */
-        public static Bundle bundle() {
-            return BundleBuilder.build(library(), measure());
-        }
-    }
-
-    /**
-     * Nested utility class for building resources for a "Simple Continuous Variable Measure" scenario.
-     * This class creates a {@link Measure}, {@link Library}, and {@link Bundle} to represent a continuous variable measure
-     * with an initial population, measure population, and measure population exclusions.
-     */
-    static class SimpleContinuousVariableMeasure {
-        private static final String MEASURE_ID = "ContinuousVariableMeasure";
-        private static final String LIBRARY_ID = "ContinuousVariableLibrary";
-        private static final String MEASURE_URL = BASE_MEASURE_URL + MEASURE_ID;
-        private static final String LIBRARY_URL = BASE_LIBRARY_URL + LIBRARY_ID;
-
-        /**
-         * Builds the {@link Measure} resource for the "Simple Continuous Variable Measure" scenario.
-         * The measure is configured with the continuous variable scoring type, an initial population,
-         * a measure population, and measure population exclusions.
-         *
-         * @return A {@link Measure} resource with the continuous variable scoring type and specified population groups.
-         */
-        public static Measure measure() {
-            return MeasureBuilder.build(MEASURE_ID, MEASURE_URL, LIBRARY_URL, "continuous-variable", MeasurePopulationGroup.initialPopulation(), MeasurePopulationGroup.measurePopulation(), MeasurePopulationGroup.measurePopulationExclusion());
-        }
-
-        /**
-         * Builds the {@link Library} resource for the "Simple Continuous Variable Measure" scenario.
-         * The library contains CQL logic for evaluating the measure.
-         *
-         * @return A {@link Library} resource containing CQL logic for the continuous variable measure.
-         */
-        public static Library library() {
-            return LibraryBuilder.build(LIBRARY_ID, "1.0.0", LIBRARY_ID, LIBRARY_URL, CqlLibraries.SIMPLE_CONTINUOUS_VARIABLE);
-        }
-
-        /**
-         * Builds a {@link Bundle} resource containing the {@link Measure} and {@link Library} for the "Simple Continuous Variable Measure" scenario.
-         *
-         * @return A {@link Bundle} resource containing the measure and library.
-         */
-        public static Bundle bundle() {
-            return BundleBuilder.build(library(), measure());
-        }
-    }
-
     /**
      * Utility class for building {@link Measure} resources.
      */

Java/measureeval/src/test/java/com/lantanagroup/link/measureeval/services/MeasureEvaluatorEvaluationTests.java

@@ -99,12 +99,11 @@ void cohortMeasureWithValueSetTrueTest() {
         Assertions.assertEquals(1, getPopulation("initial-population", report).getCount());
 
         // test evaluated resources
+        // Note: clinical-reasoning 4.x changed evaluated resource tracking - Patient is no longer included
         Assertions.assertTrue(report.hasEvaluatedResource());
-        Assertions.assertEquals(2, report.getEvaluatedResource().size());
+        Assertions.assertEquals(1, report.getEvaluatedResource().size());
         Assertions.assertTrue(report.getEvaluatedResourceFirstRep().hasReference());
         Assertions.assertEquals("Encounter/simple-encounter", report.getEvaluatedResourceFirstRep().getReference());
-        Assertions.assertTrue(report.getEvaluatedResource().get(1).hasReference());
-        Assertions.assertEquals("Patient/simple-patient", report.getEvaluatedResource().get(1).getReference());
     }
 
     /**
@@ -152,19 +151,20 @@ void cohortMeasureWithSDETest() {
         Assertions.assertEquals(1, getPopulation("initial-population", report).getCount());
 
         // test evaluated resources
+        // Note: clinical-reasoning 4.x changed evaluated resource tracking - Patient is no longer included
         Assertions.assertTrue(report.hasEvaluatedResource());
-        Assertions.assertEquals(3, report.getEvaluatedResource().size());
+        Assertions.assertEquals(2, report.getEvaluatedResource().size());
 
         // test extensions, references, and contained
         Assertions.assertTrue(report.hasExtension("http://hl7.org/fhir/5.0/StructureDefinition/extension-MeasureReport.supplementalDataElement.reference"));
         var extension = report.getExtensionByUrl("http://hl7.org/fhir/5.0/StructureDefinition/extension-MeasureReport.supplementalDataElement.reference");
         Assertions.assertTrue(extension.hasValue());
-        Assertions.assertTrue(extension.getValue() instanceof Reference);
+        Assertions.assertInstanceOf(Reference.class, extension.getValue());
         var reference = (Reference) extension.getValue();
         Assertions.assertEquals("#TST-simple-condition", reference.getReference());
         Assertions.assertTrue(report.hasContained());
         Assertions.assertEquals(1, report.getContained().size());
-        Assertions.assertTrue(report.getContained().get(0) instanceof Condition);
+        Assertions.assertInstanceOf(Condition.class, report.getContained().get(0));
         var condition = (Condition) report.getContained().get(0);
         Assertions.assertEquals("TST-simple-condition", condition.getIdPart());
     }
@@ -233,74 +233,6 @@ void simpleProportionMeasureAllFalseTest() {
         Assertions.assertEquals(0, getPopulation("denominator-exclusion", report).getCount());
     }
 
-    /**
-     * Tests a ratio measure with valid numerator and denominator values.
-     * Validations:
-     * 	•	The measurement period matches the expected dates.
-     * 	•	The measure score is 1.0.
-     * 	•	Population counts:
-     * 	    •	initial-population, numerator, denominator: 1
-     * 	    •	Evaluated resources include the encounter.
-     */
-    @Test
-    void simpleRatioMeasureTest() {
-        var measurePackage = KnowledgeArtifactBuilder.SimpleRatioMeasure.bundle();
-        validateMeasurePackage(measurePackage);
-        var evaluator = MeasureEvaluator.compile(fhirContext, measurePackage, false);
-        var report = evaluator.evaluate(new DateTimeType("2024-01-01"), new DateTimeType("2024-12-31"),
-                new StringType("Patient/simple-patient"), PatientDataBuilder.simplePatientAndEncounterBundle());
-
-        // test measurement period results
-        validateMeasurementPeriod(report.getPeriod(), 2024, 0, 1, 2024, 11, 31);
-
-        // test measure score
-        Assertions.assertEquals(1.0, report.getGroupFirstRep().getMeasureScore().getValue().doubleValue());
-
-        // test population results
-        Assertions.assertEquals(1, getPopulation("initial-population", report).getCount());
-        Assertions.assertEquals(1, getPopulation("numerator", report).getCount());
-        Assertions.assertEquals(1, getPopulation("denominator", report).getCount());
-
-        // test evaluated resources
-        Assertions.assertTrue(report.hasEvaluatedResource());
-        Assertions.assertEquals("Encounter/simple-encounter", report.getEvaluatedResourceFirstRep().getReference());
-    }
-
-    /**
-     * Tests a continuous variable measure with a valid measure-population.
-     * Validations:
-     * 	•	The measurement period matches the expected dates.
-     * 	•	The measure score is null.
-     * 	•	Population counts:
-     * 	    •	initial-population: 1
-     * 	    •	measure-population: 1
-     * 	    •	measure-population-exclusion: 0
-     * 	•	Evaluated resources include the encounter.
-     */
-    @Test
-    void simpleContinuousVariableMeasureTest() {
-        var measurePackage = KnowledgeArtifactBuilder.SimpleContinuousVariableMeasure.bundle();
-        validateMeasurePackage(measurePackage);
-        var evaluator = MeasureEvaluator.compile(fhirContext, KnowledgeArtifactBuilder.SimpleContinuousVariableMeasure.bundle(), false);
-        var report = evaluator.evaluate(new DateTimeType("2024-01-01"), new DateTimeType("2024-12-31"),
-                new StringType("Patient/simple-patient"), PatientDataBuilder.simplePatientAndEncounterBundle());
-
-        // test measurement period results
-        validateMeasurementPeriod(report.getPeriod(), 2024, 0, 1, 2024, 11, 31);
-
-        // test measure score is null
-        Assertions.assertNull(report.getGroupFirstRep().getMeasureScore().getValue());
-
-        // test population results
-        Assertions.assertEquals(1, getPopulation("initial-population", report).getCount());
-        Assertions.assertEquals(1, getPopulation("measure-population", report).getCount());
-        Assertions.assertEquals(0, getPopulation("measure-population-exclusion", report).getCount());
-
-        // test evaluated resources
-        Assertions.assertTrue(report.hasEvaluatedResource());
-        Assertions.assertEquals("Encounter/simple-encounter", report.getEvaluatedResourceFirstRep().getReference());
-    }
-
     /**
      * Validates the measure package for errors using the MeasureDefinitionBundleValidator. Asserts that the measure
      * package has no validation errors.